I have the entrez IDs of 100 proteins and I have put them in a list and been trying to use R's mgeneSim function from the GOSemSim package, but I am getting the following error:

> mgeneSim(protein_id_list, organism="human")

    <0 x 0 matrix>
    There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
    Warning messages:
    1: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'
    2: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'
    3: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'

The contents of the list are:

> protein_id_list

      [1] "O14757" "P49760" "P07333" "P48729" "O43293" "Q13627" "P11362" "P17948" "P36888" "P06241" "P49840" "P49841"
     [13] "P08069" "O60674" "P52333" ...

Even the following code fails:

> mgeneSim(c("Q9Y243", "P06213"))

    Warning messages:
    1: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'
    2: In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'

protein ID is not supported. You should use entrez gene ID.

You can convert your protein ID using `clusterProfiler::bitr` function.

> library(clusterProfiler)

> bitr('P08069', 'UNIPROT', 'ENTREZID', OrgDb='org.Hs.eg.db')
  UNIPROT ENTREZID
1  P08069     3480